Start disabling community packages until you find the cause. I suggest to restart after each /disabling/.Better to start with the packages installed recently.. If you find the package, notify the developer, with a bug report, message, or even in this thread, then they/we can fix it.

@tito: Am I correct saying that Package Control has no logging feature? Had a quick look and saw no update log file. Logging dates of auto-updates would make things a lot easier in many cases. Specially in those classic "it just suddenly started yesterday" situations.